1. Chapter 5 Protein Structure and Function

2. Amino Acids and Primary Structure • Amino acids • Amino group • Carboxyl group • R group; 20 Side chains • Peptide bond • Between NH2 and COOH • Polypeptide • A chain of amino acids • N terminus and C terminus

3. Amino Acids

4. Primary and Secondary Structure • Primary structure • _______________________________________ • Secondary structure • Core elements of protein architecture • Neutralization of partial charges of the peptide backbone by hydrogen bonding • Local folding of polypeptide chain • _____________ : 60% of the polypeptide chain • Random coils and U-shaped turn

5. a-Helix • Hydrogen bond between carbony O (n) and amid H (n+4) • Directionality on the helix : The same orientation of H bond donor • Side chains point _______ • Determine hydrophobic or hydrophilic quality

6. b-Sheet • Laterally packed b strands of 5 to 8 residue • Hydrogen bonding between b strands  b sheet, pleated sheet • Parallel or antiparallel

7. Tertiary Structure • Tertiary structure • Overall folding of a polypeptide chain • Stabilization • weak interaction • Hydrophobic interaction between nonpolar side chains • Hydrogen bond between polar side chains and peptide bonds • Disulfide bond formation

8. Graphical Representation of the Structure of Ras

9. Higher Levels of Structure • Domains • Completely folded region of polypeptide • Fundamental units of protein structure and function • Structural feature: • proline-rich, acidic • Functional feature: • DNA binding, membrane binding • e.g. lambda repressor (236 aa) • N terminal domain : DNA binding • C terminal domain : Dimerization • Interaction with C terminal domain of another molecule

10. Modular proteins • New proteins by combination of functional domains • Biotechnological application

11. Quaternary Structure • Association of multiple polypeptide chains • Lambda repressor : dimer • E. coli RNA polymerase : Five polypeptide chains

12. Disruption of Protein Structure • Factors disrupting protein sturcture • Heat, extreme pH, organic solvent, detergent • Denaturation • Complete unfolding of amino acid chain • Sometimes irreversible : e.g. boiled egg • Melting temperature (Tm) • Denaturation temperature for a given protein • Depending on protein structure • Proteins from organisms living in thermal vents

13. Examples of Protein Structure and Function • Keratin • Structural protein for hair, wool, feathers, nails, scales, hooves, horns, skin • Very strong and water insoluble • Hydrophobic alpha helices • Long a-helix with hydrophobic amino acids (A, I, V, M, F) • Forming fibers by hydrophobic interactions • Disulfide bonds • The more S-S bonds the harder the structure • Permanent wave • Reducing of disulfide bond  Generation of new disulfide bond

14. Examples of Protein Structure and Function • Lambda Repressor • Binding of N-terminal domain helix 3 to specific bases within the DNA binding sequence

15. Examples of Protein Structure and Function • Trp Repressor • If plenty of Trp in the cytosol • Binding of Trp into Trp Repressor and change the conformation • Trp repressor binds to DNA and represses expression of genes involved in Trp synthesis

16. Predicting Protein Structure • It is difficult to predict three dimensional structure from the amino acid sequence • Comparison to other proteins with known function or structure • Easy access of information through public database • NCBI (National center for Biotechnology Information) run by National Institutes of Health (NIH) • http://www.ncbi.nlm.nih.gov • Testing structure-function prediction • Using molecular biological tools

17. Protein Engineering • Manipulation of protein’s amino acid sequence to change its function or properties • Chemical manufacturing • Develop enzymes more suitable for industrial applications • Increasing enzyme stability • e.g. bacteriophage lysozyme: introduce S-S bond to increase heat resistance • Proteases in detergent